Starting phenix.real_space_refine on Thu Dec 7 16:38:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgg_16642/12_2023/8cgg_16642.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 1590 2.51 5 N 530 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 293": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2710 Number of models: 1 Model: "" Number of chains: 5 Chain: "U" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "A" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "B" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "D" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 542 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Time building chain proxies: 1.60, per 1000 atoms: 0.59 Number of scatterers: 2710 At special positions: 0 Unit cell: (67.08, 67.94, 44.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 550 8.00 N 530 7.00 C 1590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 504.7 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 590 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 303 removed outlier: 9.112A pdb=" N GLY A 298 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ASN B 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY A 300 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLN B 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN A 302 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY B 298 " --> pdb=" O ALA U 297 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU U 299 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 300 " --> pdb=" O LEU U 299 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN U 301 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLY U 298 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ASN C 301 " --> pdb=" O GLY U 298 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY U 300 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLN C 303 " --> pdb=" O GLY U 300 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN U 302 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N GLY C 298 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ASN D 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY C 300 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLN D 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN C 302 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.692A pdb=" N ASN U 306 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.687A pdb=" N MET A 311 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY B 314 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 313 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N PHE B 316 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ALA A 315 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE B 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N SER A 317 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 317 " --> pdb=" O PHE U 316 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE U 318 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET U 311 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLY C 314 " --> pdb=" O MET U 311 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE U 313 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N PHE C 316 " --> pdb=" O PHE U 313 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ALA U 315 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE C 318 " --> pdb=" O ALA U 315 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N SER U 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET C 311 " --> pdb=" O ASN D 312 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLY D 314 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE C 313 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N PHE D 316 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ALA C 315 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE D 318 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N SER C 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 331 removed outlier: 6.725A pdb=" N ALA A 321 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA B 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET A 323 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA B 326 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 325 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA B 328 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN A 327 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU B 330 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 329 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA U 321 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA C 324 " --> pdb=" O ALA U 321 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET U 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA C 326 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA U 325 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA C 328 " --> pdb=" O ALA U 325 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN U 327 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU C 330 " --> pdb=" O GLN U 327 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA U 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 321 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA D 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET C 323 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA D 326 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 325 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA D 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 327 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU D 330 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 336 removed outlier: 6.471A pdb=" N GLY A 335 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY U 335 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY C 335 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 344 through 347 removed outlier: 6.619A pdb=" N GLN A 344 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER B 347 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN A 346 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN U 344 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER C 347 " --> pdb=" O GLN U 344 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN U 346 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN C 344 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER D 347 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN C 346 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.771A pdb=" N GLN A 354 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN U 354 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN C 354 " --> pdb=" O ASN D 355 " (cutoff:3.500A) 30 hydrogen bonds defined for protein. 90 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 936 1.34 - 1.47: 704 1.47 - 1.60: 1025 1.60 - 1.73: 0 1.73 - 1.86: 80 Bond restraints: 2745 Sorted by residual: bond pdb=" C GLN D 360 " pdb=" O GLN D 360 " ideal model delta sigma weight residual 1.231 1.301 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C GLN C 360 " pdb=" O GLN C 360 " ideal model delta sigma weight residual 1.231 1.301 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C GLN U 360 " pdb=" O GLN U 360 " ideal model delta sigma weight residual 1.231 1.301 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C GLN A 360 " pdb=" O GLN A 360 " ideal model delta sigma weight residual 1.231 1.300 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C GLN B 360 " pdb=" O GLN B 360 " ideal model delta sigma weight residual 1.231 1.300 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 2740 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.45: 105 106.45 - 113.56: 1144 113.56 - 120.67: 1320 120.67 - 127.78: 1066 127.78 - 134.89: 15 Bond angle restraints: 3650 Sorted by residual: angle pdb=" N GLY D 298 " pdb=" CA GLY D 298 " pdb=" C GLY D 298 " ideal model delta sigma weight residual 110.45 116.59 -6.14 1.30e+00 5.92e-01 2.23e+01 angle pdb=" N GLY U 298 " pdb=" CA GLY U 298 " pdb=" C GLY U 298 " ideal model delta sigma weight residual 110.45 116.58 -6.13 1.30e+00 5.92e-01 2.22e+01 angle pdb=" N GLY A 298 " pdb=" CA GLY A 298 " pdb=" C GLY A 298 " ideal model delta sigma weight residual 110.45 116.58 -6.13 1.30e+00 5.92e-01 2.22e+01 angle pdb=" N GLY B 298 " pdb=" CA GLY B 298 " pdb=" C GLY B 298 " ideal model delta sigma weight residual 110.45 116.57 -6.12 1.30e+00 5.92e-01 2.22e+01 angle pdb=" N GLY C 298 " pdb=" CA GLY C 298 " pdb=" C GLY C 298 " ideal model delta sigma weight residual 110.45 116.56 -6.11 1.30e+00 5.92e-01 2.21e+01 ... (remaining 3645 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 15.37: 1351 15.37 - 30.71: 144 30.71 - 46.04: 35 46.04 - 61.37: 20 61.37 - 76.70: 10 Dihedral angle restraints: 1560 sinusoidal: 575 harmonic: 985 Sorted by residual: dihedral pdb=" CA GLN C 327 " pdb=" C GLN C 327 " pdb=" N ALA C 328 " pdb=" CA ALA C 328 " ideal model delta harmonic sigma weight residual -180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLN B 327 " pdb=" C GLN B 327 " pdb=" N ALA B 328 " pdb=" CA ALA B 328 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLN A 327 " pdb=" C GLN A 327 " pdb=" N ALA A 328 " pdb=" CA ALA A 328 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1557 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.042: 110 0.042 - 0.080: 102 0.080 - 0.119: 58 0.119 - 0.157: 30 0.157 - 0.196: 15 Chirality restraints: 315 Sorted by residual: chirality pdb=" CA LEU B 299 " pdb=" N LEU B 299 " pdb=" C LEU B 299 " pdb=" CB LEU B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA LEU D 299 " pdb=" N LEU D 299 " pdb=" C LEU D 299 " pdb=" CB LEU D 299 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA LEU C 299 " pdb=" N LEU C 299 " pdb=" C LEU C 299 " pdb=" CB LEU C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 312 not shown) Planarity restraints: 545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 334 " -0.038 2.00e-02 2.50e+03 2.54e-02 1.61e+01 pdb=" CG TRP C 334 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C 334 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 334 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 334 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 334 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 334 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 334 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 334 " -0.038 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP A 334 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 334 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 334 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 334 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 334 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 334 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 334 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 334 " -0.038 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP U 334 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP U 334 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP U 334 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP U 334 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP U 334 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP U 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 334 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP U 334 " 0.009 2.00e-02 2.50e+03 ... (remaining 542 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1721 3.09 - 3.54: 2400 3.54 - 3.99: 4064 3.99 - 4.45: 4901 4.45 - 4.90: 7677 Nonbonded interactions: 20763 Sorted by model distance: nonbonded pdb=" O ALA B 315 " pdb=" OG SER B 317 " model vdw 2.637 2.440 nonbonded pdb=" O ALA C 315 " pdb=" OG SER C 317 " model vdw 2.637 2.440 nonbonded pdb=" O ALA U 315 " pdb=" OG SER U 317 " model vdw 2.638 2.440 nonbonded pdb=" O ALA D 315 " pdb=" OG SER D 317 " model vdw 2.638 2.440 nonbonded pdb=" O ALA A 315 " pdb=" OG SER A 317 " model vdw 2.638 2.440 ... (remaining 20758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.470 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 12.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.070 2745 Z= 0.721 Angle : 1.669 7.732 3650 Z= 1.087 Chirality : 0.081 0.196 315 Planarity : 0.007 0.025 545 Dihedral : 16.619 76.701 970 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.16), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.017 TRP C 334 PHE 0.009 0.003 PHE B 313 ARG 0.001 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 1.2321 time to fit residues: 88.2709 Evaluate side-chains 67 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 345 ASN A 345 ASN B 345 ASN C 345 ASN D 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2745 Z= 0.206 Angle : 0.786 6.315 3650 Z= 0.412 Chirality : 0.039 0.114 315 Planarity : 0.002 0.010 545 Dihedral : 5.747 17.688 400 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.60 % Allowed : 8.80 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.15), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 334 PHE 0.011 0.002 PHE B 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.297 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 1.2737 time to fit residues: 84.6733 Evaluate side-chains 56 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2745 Z= 0.233 Angle : 0.787 5.583 3650 Z= 0.418 Chirality : 0.039 0.112 315 Planarity : 0.002 0.018 545 Dihedral : 5.504 18.544 400 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.80 % Allowed : 11.60 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.15), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 334 PHE 0.015 0.002 PHE C 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.254 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 1.4206 time to fit residues: 81.1971 Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2745 Z= 0.269 Angle : 0.818 5.666 3650 Z= 0.438 Chirality : 0.040 0.112 315 Planarity : 0.003 0.016 545 Dihedral : 5.562 19.310 400 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.80 % Allowed : 12.00 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.16), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP D 334 PHE 0.016 0.002 PHE U 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.294 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 1.4011 time to fit residues: 80.1379 Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2745 Z= 0.380 Angle : 0.934 6.806 3650 Z= 0.506 Chirality : 0.042 0.115 315 Planarity : 0.003 0.019 545 Dihedral : 5.901 19.889 400 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.80 % Allowed : 13.60 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.16), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP D 334 PHE 0.019 0.003 PHE C 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.289 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 1.3645 time to fit residues: 79.4654 Evaluate side-chains 56 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2745 Z= 0.238 Angle : 0.784 6.383 3650 Z= 0.416 Chirality : 0.039 0.113 315 Planarity : 0.003 0.018 545 Dihedral : 5.394 18.632 400 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.16), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 334 PHE 0.019 0.002 PHE U 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.282 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 1.4133 time to fit residues: 77.9695 Evaluate side-chains 54 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.0030 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2745 Z= 0.323 Angle : 0.879 6.362 3650 Z= 0.471 Chirality : 0.041 0.115 315 Planarity : 0.003 0.019 545 Dihedral : 5.671 19.602 400 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 15.60 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.16), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.12), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.005 TRP D 334 PHE 0.020 0.003 PHE C 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.4291 time to fit residues: 80.2127 Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 23 optimal weight: 7.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2745 Z= 0.197 Angle : 0.723 5.797 3650 Z= 0.381 Chirality : 0.038 0.113 315 Planarity : 0.002 0.017 545 Dihedral : 5.090 17.373 400 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.40 % Allowed : 15.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.17), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.13), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 334 PHE 0.018 0.002 PHE U 283 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.291 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 1.4512 time to fit residues: 79.9798 Evaluate side-chains 54 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2745 Z= 0.248 Angle : 0.796 5.936 3650 Z= 0.424 Chirality : 0.039 0.114 315 Planarity : 0.003 0.018 545 Dihedral : 5.347 19.016 400 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.17), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.13), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 334 PHE 0.021 0.002 PHE C 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.4293 time to fit residues: 80.2538 Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2745 Z= 0.291 Angle : 0.841 5.962 3650 Z= 0.451 Chirality : 0.040 0.114 315 Planarity : 0.003 0.019 545 Dihedral : 5.470 19.406 400 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.17), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.13), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 334 PHE 0.021 0.002 PHE C 283 ARG 0.001 0.000 ARG C 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.4288 time to fit residues: 80.2298 Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 0.0470 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080080 restraints weight = 2832.804| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.44 r_work: 0.3077 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2745 Z= 0.257 Angle : 0.796 5.938 3650 Z= 0.422 Chirality : 0.039 0.114 315 Planarity : 0.003 0.017 545 Dihedral : 5.329 18.551 400 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.17), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.13), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP C 334 PHE 0.022 0.002 PHE D 283 ARG 0.001 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.00 seconds wall clock time: 29 minutes 46.98 seconds (1786.98 seconds total)